Rodrigos_article
Marie
2024-06-16
Load data
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Load functions and groups
# Functions:
source(paste0(WD, "scripts/finding_the_core.R"))
source(paste0(WD, "../2023_RETHINK_sample_collection/scripts/functions/PCOA_from_long_data.R"))
source(paste0(WD, "../2023_MiDAS_OK_testing/script/ADONIS_from_long_data.R"))
# Make PCoA on the differnet taxonomic levels
source(paste0(WD, "../2023_RETHINK_sample_collection/scripts/functions/PCOA_from_long_data.R"))
source(paste0(WD, "scripts/functions/growing_dying_bar_plot.R"))
SampleContent2_colors <- c("#1e8449","#21618C","#b03a2e", "#ffb74d", "#e65100", "#795548")
# Functional groups
Nitrifiers = c("g__Nitrosomonas","g__Nitrosospira","g__Nitrospira","g__Nitrotoga")
Denitrifiers = c("g__Zoogloea", "g__Rhodoferax", "g__Thauera", "g__Rhodobacter",
"g__Sulfuritalea", "g__Paracoccus", "g__Azoarcus")
PAOs <- c(
"g__Ca_Phosphoribacter",
"g__Azonexus",
"g__Ca_Accumulibacter",
"g__Ca_Lutibacillus",
"g__Tetrasphaera",
"g__Microlunatus" )
GAOs <- c("g__Ca_Competibacter",
"g__Defluviicoccus",
"g__Propionivibrio",
"g__Micropruina",
"g__Ca_Contendobacter",
"g__Ca_Proximibacter")
Filaments <- c("g__Ca_Microthrix", "g__Leptothrix","g__Sphaerotilus","g__Ca_Villigracilis","g__Trichococcus",
"g__Thiothrix","g__Ca_Promineofilum","Haliscomenobacter","g__Gordonia","g__Sarcinithrix",
"g__Ca_Amarolinea","g__Kouleothrix","g__Ca_Alysiosphaera",
"g__Nocardioides","g__midas_g_1668","g__Anaerolinea","g__Ca_Caldilinea",
"g__Ca_Hadersleviella","g__midas_g_344",
"g__Skermania","g__Ca_Nostocoida","g__Neomegalonema","g__Beggiatoa",
"g__Ca_Brevefilum")
df_functional <-
tibble(Genus = c(Nitrifiers, Denitrifiers, PAOs, GAOs, Filaments),
functional_group = c(rep("Nitrifiers", length(Nitrifiers)),
rep("Denitrifiers", length(Denitrifiers)),
rep("PAOs", length(PAOs)),
rep("GAOs", length(GAOs)),
rep("Filaments", length(Filaments))
))Save ampvis data to Rodrigo
Ordinations of sewer envionements (genus level)
Biofilm only
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HM at the genus level: top 15 for each system
Figure XX: Most abundant genera across sewer envionments merged sample sites
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Figure XX: Most abundant genera across sewer envionments per sample site
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HM at the genus level: top 15 for each system –> also SWW
Figure XX: Most abundant genera across sewer envionments merged sample sites
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PAOs and GAOs in the sewer
Figure SXX: Heatmap of PAO and GAOs merged samplesites
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Figure SXX: Heatmap of PAO and GAOs for each samplesite
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Each site by date
Figure XX: Biofilm (g)
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Figure XX: Biofilm (p.)
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Figure XX: Biofilm (e.p.)
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Most abundant genera by date
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